MultiQC Quality Control Report for the PRJNA658001 RNA-seq Dataset

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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        This report was generated using MultiQC, version 1.27

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        MultiQC Quality Control Report for the PRJNA658001 RNA-seq Dataset

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-11-15, 23:24 CET based on data in: /data/jwd06/main/091/832/91832262/working/multiqc_WDir

        Because this report contains a lot of samples, you may need to click 'Show plot' to see some graphs.

        General Statistics

        Showing 144/144 rows and 5/7 columns.
        Sample Name% Duplication% > Q30Mb Q30 basesReads After FilteringGC content% PF% Adapter
        SRR12475103
        58.4%
        97.2%
        4709.6Mb
        34.9M
        47.9%
        100.0%
        0.0%
        SRR12475104
        31.2%
        97.3%
        2950.3Mb
        22.0M
        53.0%
        100.0%
        0.0%
        SRR12475105
        33.7%
        97.0%
        2805.4Mb
        20.7M
        52.5%
        100.0%
        0.0%
        SRR12475106
        20.0%
        97.5%
        2767.7Mb
        20.6M
        57.0%
        100.0%
        0.0%
        SRR12475107
        25.2%
        97.5%
        3619.7Mb
        27.5M
        53.2%
        100.0%
        0.0%
        SRR12475108
        34.3%
        97.0%
        4570.1Mb
        34.2M
        49.7%
        100.0%
        0.0%
        SRR12475109
        21.1%
        97.5%
        5617.9Mb
        41.7M
        51.2%
        100.0%
        0.0%
        SRR12475110
        27.1%
        97.3%
        6919.4Mb
        51.5M
        50.7%
        100.0%
        0.0%
        SRR12475111
        21.9%
        97.5%
        6141.4Mb
        45.6M
        51.0%
        100.0%
        0.0%
        SRR12475112
        25.6%
        97.5%
        9155.4Mb
        69.0M
        49.4%
        100.0%
        0.0%
        SRR12475113
        18.2%
        97.5%
        7512.3Mb
        56.6M
        49.8%
        96.2%
        26.5%
        SRR12475114
        18.3%
        97.5%
        11623.5Mb
        86.3M
        49.9%
        96.3%
        22.8%
        SRR12475115
        18.6%
        97.3%
        6984.0Mb
        51.7M
        50.0%
        94.8%
        21.0%
        SRR12475116
        18.4%
        97.3%
        9704.9Mb
        72.1M
        49.8%
        95.8%
        22.1%
        SRR12475117
        20.3%
        97.5%
        7340.0Mb
        54.4M
        50.0%
        96.0%
        22.5%
        SRR12475118
        18.9%
        96.5%
        7016.0Mb
        52.2M
        50.7%
        94.2%
        18.8%
        SRR12475119
        17.4%
        97.4%
        7662.9Mb
        56.9M
        51.5%
        95.9%
        22.6%
        SRR12475120
        19.4%
        97.4%
        7424.8Mb
        56.2M
        49.9%
        95.1%
        27.1%
        SRR12475121
        20.8%
        97.3%
        6935.6Mb
        51.5M
        50.3%
        95.6%
        22.9%
        SRR12475122
        17.3%
        97.4%
        7789.3Mb
        58.1M
        50.7%
        96.5%
        23.4%
        SRR12475123
        19.6%
        97.5%
        4543.9Mb
        33.7M
        54.3%
        94.3%
        21.4%
        SRR12475124
        12.0%
        97.0%
        1001.9Mb
        8.6M
        55.4%
        66.0%
        42.1%
        SRR12475125
        15.3%
        97.6%
        4109.7Mb
        30.5M
        56.6%
        93.3%
        23.2%
        SRR12475126
        16.8%
        97.6%
        4830.7Mb
        35.7M
        55.9%
        93.4%
        23.3%
        SRR12475127
        12.3%
        97.4%
        1592.5Mb
        12.1M
        57.5%
        87.4%
        22.3%
        SRR12475128
        16.6%
        97.7%
        5113.0Mb
        37.9M
        55.8%
        94.4%
        24.2%
        SRR12475129
        16.1%
        97.4%
        9030.8Mb
        67.2M
        50.1%
        96.6%
        24.6%
        SRR12475130
        18.0%
        97.4%
        5501.3Mb
        41.4M
        49.9%
        96.5%
        26.3%
        SRR12475131
        19.6%
        97.2%
        7171.9Mb
        53.7M
        49.4%
        95.6%
        23.7%
        SRR12475132
        16.3%
        97.4%
        8332.8Mb
        62.4M
        50.6%
        95.9%
        25.1%
        SRR12475133
        17.7%
        97.5%
        7750.3Mb
        58.9M
        49.7%
        95.2%
        30.0%
        SRR12475134
        19.4%
        97.4%
        7173.9Mb
        54.4M
        50.1%
        94.1%
        28.3%
        SRR12475135
        19.5%
        97.4%
        6804.6Mb
        51.3M
        48.9%
        94.4%
        27.5%
        SRR12475136
        29.7%
        97.4%
        6985.1Mb
        54.0M
        48.4%
        93.2%
        32.3%
        SRR12475137
        17.8%
        97.4%
        6688.9Mb
        50.8M
        49.8%
        94.8%
        27.8%
        SRR12475138
        17.5%
        97.6%
        8108.2Mb
        61.0M
        49.9%
        95.5%
        27.8%
        SRR12475139
        27.2%
        97.3%
        5292.0Mb
        40.7M
        48.1%
        92.4%
        29.8%
        SRR12475140
        18.0%
        97.3%
        5658.7Mb
        42.5M
        49.3%
        92.2%
        25.9%
        SRR12475141
        18.2%
        97.3%
        2791.7Mb
        20.9M
        54.6%
        87.6%
        24.4%
        SRR12475142
        15.3%
        97.5%
        1872.1Mb
        13.8M
        58.6%
        86.6%
        19.9%
        SRR12475143
        15.8%
        96.9%
        3153.2Mb
        23.8M
        57.0%
        91.6%
        25.1%
        SRR12475144
        15.7%
        97.7%
        5678.6Mb
        42.0M
        57.1%
        94.3%
        22.7%
        SRR12475145
        20.4%
        97.3%
        1880.3Mb
        14.1M
        54.5%
        84.3%
        22.4%
        SRR12475146
        18.9%
        97.4%
        2147.9Mb
        16.2M
        55.5%
        86.6%
        24.2%
        SRR12475147
        23.6%
        97.2%
        5578.2Mb
        41.8M
        50.1%
        93.6%
        23.9%
        SRR12475148
        33.4%
        97.3%
        4278.6Mb
        32.5M
        48.8%
        92.1%
        27.1%
        SRR12475149
        18.0%
        97.5%
        6794.2Mb
        51.3M
        52.1%
        93.8%
        25.9%
        SRR12475150
        17.3%
        97.6%
        5897.7Mb
        44.1M
        53.2%
        94.5%
        25.1%
        SRR12475151
        16.2%
        98.2%
        3225.8Mb
        27.9M
        53.4%
        92.7%
        55.4%
        SRR12475152
        16.8%
        98.2%
        2756.3Mb
        24.1M
        53.0%
        91.2%
        56.8%
        SRR12475153
        13.3%
        97.9%
        1375.1Mb
        12.4M
        55.4%
        81.3%
        57.9%
        SRR12475154
        12.5%
        98.2%
        2258.8Mb
        21.4M
        55.5%
        80.7%
        67.3%
        SRR12475155
        10.3%
        97.4%
        799.7Mb
        7.4M
        54.6%
        71.6%
        56.2%
        SRR12475156
        15.4%
        97.9%
        1497.2Mb
        13.4M
        53.2%
        79.8%
        59.2%
        SRR12475157
        11.7%
        97.3%
        969.4Mb
        8.2M
        56.3%
        78.2%
        37.2%
        SRR12475158
        12.3%
        98.1%
        2441.6Mb
        22.7M
        55.3%
        81.5%
        63.9%
        SRR12475159
        14.1%
        98.3%
        3823.1Mb
        34.7M
        52.0%
        90.6%
        62.8%
        SRR12475160
        16.3%
        98.2%
        3534.8Mb
        31.2M
        53.1%
        86.8%
        58.9%
        SRR12475161
        16.5%
        98.3%
        4696.2Mb
        41.2M
        52.0%
        91.6%
        59.1%
        SRR12475162
        16.1%
        98.3%
        3904.1Mb
        34.2M
        52.1%
        92.3%
        59.5%
        SRR12475163
        15.4%
        97.9%
        3651.4Mb
        32.7M
        51.8%
        91.5%
        59.8%
        SRR12475164
        14.7%
        97.9%
        3053.9Mb
        27.3M
        52.3%
        89.8%
        60.1%
        SRR12475165
        12.5%
        98.2%
        4862.0Mb
        49.1M
        52.7%
        89.0%
        77.3%
        SRR12475166
        12.7%
        98.3%
        4306.1Mb
        44.5M
        53.6%
        91.2%
        78.7%
        SRR12475167
        14.3%
        98.1%
        4370.5Mb
        41.7M
        53.3%
        94.4%
        71.2%
        SRR12475168
        14.6%
        98.1%
        3906.3Mb
        36.0M
        53.4%
        94.0%
        67.7%
        SRR12475169
        13.8%
        98.1%
        3477.4Mb
        32.8M
        54.6%
        93.5%
        68.9%
        SRR12475170
        15.4%
        98.1%
        4121.0Mb
        38.3M
        54.4%
        94.2%
        68.3%
        SRR12475171
        15.2%
        98.1%
        3585.3Mb
        33.5M
        54.6%
        94.6%
        68.2%
        SRR12475172
        24.6%
        98.1%
        1490.7Mb
        15.6M
        49.2%
        75.7%
        83.3%
        SRR12475173
        14.2%
        98.1%
        3260.9Mb
        31.4M
        54.3%
        93.0%
        71.4%
        SRR12475174
        13.9%
        98.1%
        2816.1Mb
        28.2M
        54.3%
        87.3%
        76.0%
        SRR12475175
        22.3%
        97.4%
        4440.8Mb
        33.0M
        50.7%
        94.7%
        21.0%
        SRR12475176
        34.1%
        97.2%
        4493.4Mb
        33.6M
        49.6%
        92.3%
        23.5%
        SRR12475177
        20.3%
        97.5%
        4870.6Mb
        36.2M
        51.5%
        95.7%
        22.1%
        SRR12475178
        20.2%
        97.5%
        4752.9Mb
        35.7M
        53.3%
        94.8%
        23.3%
        SRR12475179
        21.9%
        97.3%
        5410.4Mb
        40.3M
        51.2%
        95.5%
        22.0%
        SRR12475180
        29.5%
        97.2%
        4391.3Mb
        32.8M
        50.0%
        94.2%
        22.3%
        SRR12475181
        21.6%
        97.4%
        6171.8Mb
        45.7M
        51.1%
        95.3%
        22.2%
        SRR12475182
        31.1%
        97.3%
        4866.8Mb
        36.0M
        50.3%
        93.5%
        21.0%
        SRR12475183
        28.2%
        97.1%
        4158.6Mb
        31.2M
        48.2%
        93.8%
        21.7%
        SRR12475184
        20.4%
        97.4%
        8368.2Mb
        62.4M
        49.6%
        96.8%
        24.6%
        SRR12475185
        17.0%
        97.5%
        8046.6Mb
        59.6M
        50.6%
        97.0%
        22.6%
        SRR12475186
        18.3%
        97.5%
        7438.2Mb
        54.8M
        50.6%
        96.5%
        21.1%
        SRR12475187
        17.6%
        97.4%
        6615.9Mb
        49.7M
        50.5%
        96.1%
        24.8%
        SRR12475188
        19.5%
        97.5%
        7282.3Mb
        54.9M
        49.7%
        96.6%
        27.1%
        SRR12475189
        16.9%
        97.4%
        4768.6Mb
        35.5M
        53.2%
        94.8%
        22.4%
        SRR12475190
        17.4%
        97.5%
        5041.6Mb
        37.3M
        53.9%
        94.7%
        22.4%
        SRR12475191
        17.4%
        97.5%
        4372.1Mb
        32.1M
        56.4%
        93.5%
        19.9%
        SRR12475192
        17.9%
        97.6%
        3023.0Mb
        22.4M
        54.9%
        92.5%
        22.0%
        SRR12475193
        19.6%
        97.5%
        4883.9Mb
        36.1M
        55.5%
        94.3%
        22.5%
        SRR12475194
        17.9%
        97.6%
        3595.9Mb
        26.4M
        56.7%
        93.5%
        19.5%
        SRR12475195
        18.6%
        97.5%
        4595.1Mb
        34.1M
        54.7%
        94.5%
        22.0%
        SRR12475196
        19.0%
        97.6%
        5749.4Mb
        42.3M
        53.9%
        95.3%
        21.5%
        SRR12475197
        19.2%
        97.5%
        5860.1Mb
        43.4M
        54.3%
        94.7%
        22.4%
        SRR12475198
        16.2%
        97.4%
        3926.5Mb
        29.0M
        55.7%
        93.6%
        20.4%
        SRR12475199
        16.4%
        97.6%
        4275.4Mb
        31.3M
        57.1%
        94.0%
        19.4%
        SRR12475200
        17.9%
        97.6%
        5752.2Mb
        42.1M
        56.0%
        95.5%
        19.8%
        SRR12475201
        20.3%
        97.7%
        8581.9Mb
        63.1M
        54.0%
        96.1%
        21.6%
        SRR12475202
        17.9%
        97.7%
        3904.4Mb
        28.7M
        56.9%
        93.2%
        21.4%
        SRR12475203
        17.2%
        97.6%
        5479.0Mb
        40.4M
        55.6%
        95.0%
        22.2%
        SRR12475204
        14.4%
        97.6%
        3582.0Mb
        26.9M
        57.2%
        92.9%
        24.6%
        SRR12475205
        17.6%
        97.5%
        4091.2Mb
        30.3M
        56.4%
        92.7%
        22.1%
        SRR12475206
        19.4%
        97.7%
        5590.4Mb
        41.5M
        56.0%
        93.8%
        23.8%
        SRR12475207
        23.8%
        97.4%
        4586.6Mb
        34.3M
        52.6%
        93.3%
        24.0%
        SRR12475208
        20.7%
        97.5%
        5007.7Mb
        37.3M
        53.4%
        93.2%
        24.0%
        SRR12475209
        18.5%
        97.5%
        4583.8Mb
        34.1M
        54.4%
        92.8%
        23.6%
        SRR12475210
        16.5%
        97.6%
        3892.2Mb
        29.3M
        55.5%
        93.4%
        26.9%
        SRR12475211
        22.6%
        97.5%
        3448.3Mb
        25.8M
        54.2%
        90.4%
        24.5%
        SRR12475212
        17.1%
        97.7%
        4977.1Mb
        37.0M
        58.6%
        94.1%
        24.1%
        SRR12475213
        23.3%
        97.4%
        3158.3Mb
        23.8M
        53.8%
        90.4%
        25.0%
        SRR12475214
        20.8%
        97.4%
        3547.0Mb
        26.7M
        54.0%
        92.4%
        25.0%
        SRR12475215
        18.6%
        97.5%
        5238.6Mb
        39.2M
        54.5%
        93.6%
        24.5%
        SRR12475216
        15.9%
        97.6%
        3711.4Mb
        27.6M
        55.8%
        93.2%
        23.9%
        SRR12475217
        19.4%
        97.4%
        4346.8Mb
        32.5M
        54.9%
        92.3%
        23.4%
        SRR12475218
        27.0%
        97.2%
        3790.4Mb
        28.3M
        51.9%
        91.7%
        22.7%
        SRR12475219
        27.6%
        97.4%
        6135.6Mb
        45.7M
        51.2%
        93.3%
        21.6%
        SRR12475220
        33.8%
        97.3%
        5706.7Mb
        42.9M
        48.8%
        94.4%
        24.5%
        SRR12475221
        22.0%
        97.6%
        7008.8Mb
        52.2M
        51.3%
        94.5%
        23.8%
        SRR12475222
        19.7%
        97.5%
        6077.9Mb
        45.5M
        51.7%
        94.7%
        25.0%
        SRR12475223
        17.6%
        98.3%
        3721.6Mb
        32.2M
        52.3%
        93.0%
        56.7%
        SRR12475224
        18.0%
        98.2%
        3441.3Mb
        29.9M
        51.0%
        92.8%
        56.3%
        SRR12475225
        15.0%
        98.2%
        2617.1Mb
        23.7M
        54.6%
        89.9%
        61.3%
        SRR12475226
        13.7%
        98.1%
        2373.7Mb
        21.3M
        57.1%
        88.5%
        58.7%
        SRR12475227
        16.2%
        98.1%
        2458.6Mb
        22.1M
        53.5%
        88.8%
        59.9%
        SRR12475228
        18.5%
        98.1%
        1864.5Mb
        17.2M
        52.8%
        86.2%
        63.6%
        SRR12475229
        14.2%
        98.1%
        3086.2Mb
        27.9M
        56.1%
        86.4%
        61.3%
        SRR12475230
        16.1%
        98.1%
        2856.5Mb
        25.0M
        54.4%
        90.8%
        57.2%
        SRR12475231
        16.8%
        98.3%
        4220.5Mb
        37.5M
        50.8%
        90.7%
        59.1%
        SRR12475232
        18.0%
        98.3%
        3776.3Mb
        32.9M
        50.9%
        93.5%
        55.6%
        SRR12475233
        18.5%
        98.3%
        4407.3Mb
        37.8M
        50.8%
        93.7%
        54.9%
        SRR12475234
        17.3%
        98.3%
        3736.9Mb
        32.7M
        51.6%
        92.8%
        56.7%
        SRR12475235
        18.5%
        97.8%
        2935.0Mb
        25.6M
        50.2%
        91.3%
        56.0%
        SRR12475236
        16.8%
        97.8%
        2115.9Mb
        18.9M
        51.8%
        90.0%
        56.6%
        SRR12475237
        15.1%
        98.1%
        4093.5Mb
        39.0M
        54.8%
        93.1%
        72.2%
        SRR12475238
        13.9%
        98.2%
        4033.4Mb
        39.4M
        54.1%
        91.0%
        74.5%
        SRR12475239
        15.3%
        98.1%
        3691.3Mb
        34.5M
        54.5%
        91.7%
        70.2%
        SRR12475240
        15.1%
        98.1%
        3505.3Mb
        32.4M
        53.8%
        90.4%
        69.4%
        SRR12475241
        13.5%
        98.1%
        3195.7Mb
        31.3M
        54.6%
        89.2%
        73.8%
        SRR12475242
        15.1%
        98.0%
        3439.3Mb
        32.2M
        54.5%
        94.0%
        68.4%
        SRR12475243
        15.5%
        98.0%
        3295.4Mb
        30.2M
        54.9%
        94.5%
        66.4%
        SRR12475244
        15.1%
        98.0%
        2215.5Mb
        20.9M
        54.6%
        86.6%
        70.2%
        SRR12475245
        13.9%
        98.1%
        3222.5Mb
        31.1M
        55.7%
        91.9%
        72.2%
        SRR12475246
        14.0%
        98.1%
        2682.5Mb
        26.8M
        54.1%
        88.6%
        75.9%

        fastp

        Version: 1.0.1

        All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560

        Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.

        Filtered Reads

        Filtering statistics of sampled reads.

        Created with MultiQC

        Insert Sizes

        Insert size estimation of sampled reads.

        Created with MultiQC

        Sequence Quality

        Average sequencing quality over each base of all reads.

        Created with MultiQC

        GC Content

        Average GC content over each base of all reads.

        Created with MultiQC

        N content

        Average N content over each base of all reads.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of occurrences across all samples.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        85
        2082115
        0.0576%
        AGAGATCGGAAGAGCGTCGT
        84
        1916976
        0.0438%
        GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCG
        108
        1779699
        0.0617%
        CCAGATCGGAAGAGCGTCGT
        85
        1653384
        0.0377%
        GCAGATCGGAAGAGCGTCGT
        84
        1565783
        0.0357%
        AAGATCGGAAGAGCGTCGTG
        84
        1563067
        0.0365%
        TAGATCGGAAGAGCGTCGTG
        85
        1478256
        0.0329%
        ACAGATCGGAAGAGCGTCGT
        85
        1444424
        0.0325%
        GGAGATCGGAAGAGCGTCGT
        77
        1021302
        0.0238%
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        85
        894792
        0.0231%
        TGAGATCGGAAGAGCGTCGT
        68
        885548
        0.0193%
        CGAGATCGGAAGAGCGTCGT
        65
        767526
        0.0184%
        AAAAAAAAAA
        29
        726498
        0.0161%
        TTTTTTTTTT
        23
        695182
        0.0132%
        CAGATCGGAAGAGCGTCGTG
        76
        561888
        0.0130%
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        8
        478335
        0.0089%
        GAGATCGGAAGAGCGTCGTG
        34
        473974
        0.0110%
        CAAGATCGGAAGAGCGTCGT
        35
        434704
        0.0090%
        AAAGATCGGAAGAGCGTCGT
        28
        412976
        0.0079%
        GAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCT
        86
        350890
        0.0081%

        Overrepresented Sequences

        Overrepresented sequences in the reads.


        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        fastp1.0.1